babessell1/FastqToGeneCounts Fork of HelikarLab/FastqToGeneCounts

Snakemake pipeline for use in computing cluster to pull RNA-seq fastq reads from GEO, trim, run quality checks and align. Output interfaces with MADRID

Language: Python - Size: 2.25 MB - Last synced: about 4 hours ago - Pushed: about 5 hours ago - Stars: 0 - Forks: 0

babessell1/melt-docker-sva

Language: Shell - Size: 10.7 KB - Last synced: about 4 hours ago - Pushed: about 5 hours ago - Stars: 1 - Forks: 0

babessell1/MADRID Fork of HelikarLab/COMO

Metabolic Drug Repurposing Pipeline

Language: Python - Size: 733 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 0

babessell1/pyZINQ

Language: Jupyter Notebook - Size: 45.9 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

babessell1/tibanna-scheduler

Tibanna workflow submission scheduler

Language: Python - Size: 67.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 1

babessell1/str_sandbox

Sandbox for exploring various ideas related to tandem repeats

Language: Jupyter Notebook - Size: 30.3 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

babessell1/str-experiments

Language: Jupyter Notebook - Size: 609 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

babessell1/AluNet

Weighted Leiden algorithm for modeling Alu-mediated enhancer-promoter interaction networks

Language: HTML - Size: 8.04 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 1

babessell1/STRonvoli

CNN for enhancing short read STR calls

Language: Jupyter Notebook - Size: 45.4 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

babessell1/STRipe

Language: Jupyter Notebook - Size: 402 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

babessell1/MetReFIT

Brute force algorithm for finding biosynthetic gaps in COBRA formated constraint-based metabolic models. Can provide models or reaction databases of related species with relative scores on how closely related they are to attempt to fill in gaps. Handles reactions from multiple databases including KEGG, modelSEED, and MetaCyc to attempt to fill.

Language: MATLAB - Size: 120 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

babessell1/ExpansionHunterDenovo-LRDN Fork of rashidalabri/ExpansionHunterDenovo-LRDN

A tool for local read depth normalization of ExpansionHunter denovo calls.

Language: Python - Size: 20.5 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

babessell1/strling-docker

Automated Docker containerization for STRling

Language: Shell - Size: 36.1 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

babessell1/melt-docker-L1

Language: Shell - Size: 4.88 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

babessell1/melt-docker-alu

Language: Shell - Size: 1.95 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

babessell1/504GitExercise Fork of jwschroeder3/504GitExercise

Code to demonstrate simple use of github

Language: Python - Size: 5.86 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

babessell1/ehdn-docker

docker for running expansion hunter de novo through cwl

Language: Shell - Size: 23.4 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

babessell1/melt-docker Fork of Sop51/melt-docker

Language: Shell - Size: 52.7 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

babessell1/strling-generic

Language: Python - Size: 9.77 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

babessell1/index-docker

Language: Shell - Size: 2.93 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

babessell1/awsf3-dev-docker

Language: Shell - Size: 51.8 KB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

babessell1/tibanna Fork of 4dn-dcic/tibanna

fix awsf3

Language: Python - Size: 134 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

babessell1/bioinf545_project

Language: R - Size: 4.96 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 2

babessell1/diego-garcia-native-rezoning

For my friend's thesis project. An interactive Dash webapp for natives who were forced off their home of Diego Garcia to redesign the island plan how they would want it if given the opportunity to go home.

Language: Python - Size: 1.15 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

babessell1/auto-tsi

Library for reading LiDAR scan reads from ROS and Mission Planner telemetry outputs to calculate and map geometric/geographic properties of understory trees which cannot be measured from arial imaging.

Language: Python - Size: 33.2 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

babessell1/mei_metrics

Language: Python - Size: 44.9 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

babessell1/ExpHunterPipe

Language: Python - Size: 4.88 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

babessell1/optlang Fork of opencobra/optlang

optlang - experimenting with fixing seeds

Language: Python - Size: 9.45 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

babessell1/troppo Fork of BioSystemsUM/troppo

Reconstruction algorithms for Python (allow negative values in imat)

Language: Python - Size: 10.3 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

babessell1/cobamp Fork of BioSystemsUM/cobamp

Constraint-based modeling framework for the enumeration of pathway analysis concepts

Language: Jupyter Notebook - Size: 9.82 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

babessell1/zFPKM Fork of ronammar/zFPKM

Finding the active genes in RNA-seq gene expression studies

Language: R - Size: 258 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

babessell1/rpy2-docker Fork of rpy2/rpy2-docker

Running rpy2 in Docker containers

Language: Shell - Size: 108 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

babessell1/RogueLight

Rogue-like game written in Python using libtcod, core gameplay mechanic is centered around limited lighting resources.

Language: Python - Size: 123 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

babessell1/WeatherStation

Arduino controlled weather station I made for a course I took

Language: C++ - Size: 2.93 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

babessell1/OptionalAdvantage

Small project I did over spring break. Pulls stock information from Yahoo and uses the Black–Scholes equation to determine the best call and put contracts.

Language: Python - Size: 8.79 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

babessell1/Rosalind

Workspace for completing Rosalind Problems

Language: Python - Size: 42 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

babessell1/Master

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0